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<h1>The nairn-mpm-fea Project Source Code Organization</h1>

<p>Assuming that checked out folder's name is <code>nairn-mpm-fea</code>, the NairnMPM,  NairnFEA, Documentation, and Visualization source code is organized into various directories. The contents of the directories are:
</p>

<dl>

<dt><code>nairn-mpm-fea/Common</code></dt>
<dd>This folder has items common to both MPM and FEA code

<dl>
<dt><code>/Projects</code></dt>
<dd>This folder has XCode and Visual Studio project files for editing and compiling the code.</dd>

<dt><code>/(other folder)</code></dt>
<dd>All other folders in <code>Common</code> have various common sections of code.</dd>
</dl>

</dd>


<dt><code>nairn-mpm-fea/NairnMPM</code></dt>
<dd>This folder is the root folder for the NairnMPM source code

<dl>
<dt><code>/src</code></dt>
<dd>This folder has all MPM-specific source code in various subfolders</dd>


<dt><code>/build</code></dt>
<dd>This folder has the <code>makefile</code> for compiling the code using a <code>make</code> command.</dd>

<dt><code>/input</code></dt>
<dd>This folder has sample input files and the <code>NairnMPM.dtd</code> file. The compiled code gets installed here ready for running with the input files.

<dl>
<dt><code>/Scripted_Input</code></dt>
<dd>This folder has scripted input files that can be run using with <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPM">NairnFEAMPM</a> or <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPMViz">NairnFEAMPMViz</a> applications.</dd>

<dt><code>/XML_Input</code></dt>
<dd>This folder has XML input files that can be run from a command line. It is recommended that you rarely use such files and instead do all calculations using the scripting tools in <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPM">NairnFEAMPM</a> and <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPMViz">NairnFEAMPMViz</a>.</dd>

</dl>

</dd>

<dt><code>/tools</code></dt>
<dd>This folder has source code for command line tools that can be used with NairnMPM such as for extracting data from archive files or for comparing global results files.</dd>

</dl>

</dd>

<dt><code>nairn-mpm-fea/NairnFEA</code></dt>
<dd>This folder is the root folder for the NairnFEA source code

<dl>
<dt><code>/src</code></dt>
<dd>This folder has all FEA-specific source code in various subfolders</dd>


<dt><code>/build</code></dt>
<dd>This folder has the <code>makefile</code> for compiling the code using a <code>make</code> command.</dd>

<dt><code>/input</code></dt>
<dd>This folder has sample input files and the <code>NairnFEA.dtd</code> file. The compiled code gets installed here ready for running with the input files.

<dl>
<dt><code>/Scripted_Input</code></dt>
<dd>This folder has scripted input files that can be run using with <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPM">NairnFEAMPM</a> or <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPMViz">NairnFEAMPMViz</a> applications.</dd>

<dt><code>/XML_Input</code></dt>
<dd>This folder has XML input files that can be run from a command line. It is recommended that you rarely use such files and instead do all calculations using the scripting tools in <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPM">NairnFEAMPM</a> and <a href="http://osupdocs.forestry.oregonstate.edu/index.php/NairnFEAMPMViz">NairnFEAMPMViz</a>.</dd>

</dl>
</dd>

</dl>

</dd>

<dt><code>nairn-mpm-fea/Visualization</code></dt>
<dd>This folder is the root folder for the platform-independent, Java-based visualization tool.

<dl>
<dt><code>/src</code></dt>
<dd>This folder has the Java source code for the visualization tool called NairnFEAMPMViz.</dd>


<dt><code>/build</code></dt>
<dd>This folder has a <code>makejar</code> script that can compile the Java source code into a jar file. It also has files for creating a Windows shortcut with a provided icon.</dd>

<dt><code>/MatLab_VTK_Viz</code></dt>
<dd>Miscellaneous scripts for using MatLab to visualize results include some scripts to read VTK files.</dd>

<dt><code>/R_Tools</code></dt>
<dd>Miscellaneous scripts for using R to visualize data.</dd>

</dl>

</dd>

<dt><code>nairn-mpm-fea/Documentation</code></dt>
<dd>This folder has all minimal documentation of the current version and links to tech note <code>pdf</code> files. Open the <code>index.html</code> file to view the documentation in any browser.

<dl>
<dt><code>/TechNotes</code></dt>
<dd>This folder has a selection of tech notes as <code>pdf</code> files.</dd>
</dl>
</dd>

</dl>

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